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SpectriPy: Criss-Crossing R and Python for Powerful Mass Spectrometry Data Analysis Workflows

License: CC BY-NC-SA 4.0 docker pullsDocker Image Version (latest by date) DOI

🐍 Welcome to the SpectriPy package demo

  • 🎯 show how R and Python MS data analysis methods can be combined in a single (interactive) workflow.
  • 🔀 combine R and Python code for:
    • chromatographic peak detection of an untargeted LC-MS/MS data file
    • extract and process MS2 spectra for detected chromatographic peaks
    • download and process public reference MS2 data
    • calculate similarity between experimental and reference MS2 spectra

🛠️ Installation

Running through docker

The workflow file along with an R runtime environment including all required packages and the RStudio (Posit) editor are all bundled in a docker container.

After installation, this docker container can be run on the computer and the code and examples from the vignettes can be evaluated within this environment (without the need to install any additional packages or files).

  • If you don’t already have, install docker. Find installation information here.
  • Get the docker image of this tutorial e.g. from the command line with:
docker pull jorainer/spectripyworkshop:RELEASE_3_23
  • This will download the docker container with all software/packages based on Bioconductor release 3.23.
  • Start the docker container, either through the Docker Desktop, or on the command line with
docker run -e PASSWORD=bioc -p 8787:8787 jorainer/spectripyworkshop:RELEASE_3_23
  • Enter http://localhost:8787 in a web browser and log in with username rstudio and password bioc.
  • In the RStudio server version: open any of the Quarto files in the vignettes folder and evaluate the R code blocks in that document.

Running locally

To install all required libraries locally:

install.packages("remotes")
install.packages("BiocManager")
BiocManager::install("jorainer/SpectriPyWorkshop", dependencies = TRUE)

📌 Reproducibility & Updates

We strive for reproducibility. This workflows is designed to remain stable over time, allowing you to run the vignette also in future.

  • Major updates will be documented here.

🤝 Contribution

Interested in contributing? Please check out the RforMassSpectrometry Contributions Guide.

📜 Code of Conduct

We follow the RforMassSpectrometry Code of Conduct to maintain an inclusive and respectful community.